Sequences from the mitochondrial cytochrome b gene （Cyt b） were determined for 25 species from the superfamily Acridoidae and the homologous sequences of 19 species of grasshoppers were downloaded from the GenBank d...Sequences from the mitochondrial cytochrome b gene （Cyt b） were determined for 25 species from the superfamily Acridoidae and the homologous sequences of 19 species of grasshoppers were downloaded from the GenBank data library. The purpose was to develop a molecular phylogeny of the Acrypteridae, and to interpret the phylogenetic position of the family within the superfamily Acridoidea. Phylogeny was reconstructed by Maximum-parsimony （MP） and Bayesian criteria using Yunnanites coriacea and Tagasta marginella as outgroups. The alignment length of the fragments was 384 bp after excluding ambiguous sites, including 167 parsimony informative sites. In the fragments, the percentages of A ＋ T and G ＋ C were 70.7% and 29.3%, respectively. The monophyly of Arcypteridae is not supported by phylogenetic trees. Within the Arcypteridae, neither Arcypterinae nor Ceracrinae is supported as a monophyletic group. The current genus Chorthippus is not a monophyletic group, and should be a polyphyletic group. The present results are significantly different from the classification scheme of Arcypteridae, which is based on morphology.展开更多
We describe an interactive viewer for the All-Species Living Tree（LVTree）. The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxo...We describe an interactive viewer for the All-Species Living Tree（LVTree）. The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16 S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner.In view of the fact that the present prokaryotic systematics is largely based on 16 S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla（Proteobacteria and Firmicutes） to monophyletic clusters.展开更多
Nineteen taxa representing 10 genera of Sisoridae were subjected to phylogenetic analyses of sequence data for the nuclear genes Plagl2 and ADNP and the mitochondrial gene cytochrome b. The three data sets were analyz...Nineteen taxa representing 10 genera of Sisoridae were subjected to phylogenetic analyses of sequence data for the nuclear genes Plagl2 and ADNP and the mitochondrial gene cytochrome b. The three data sets were analyzed separately and combined into a single data set to reconstruct phylogenetic relationships among Chinese sisorids. Both Chinese Sisoridae as a whole and the glyptosternoid taxa formed monophyletic groups. The genus Pseudecheneis is likely to be the earliest diverging extant genus among the Chinese Sisoridae. The four Pareuchiloglanis species included in the study formed a monophyletic group. Glaridoglanis was indicated to be earliest diverging glyptosternoid, followed by Glyptosternon maculatum and Exostoma labiatum. Our data supported the conclusion that Oreoglanis and Pseudexostoma both formed a monophyletic group. On the basis of the fossil record and the results of a molecular dating analysis, we estimated that the Sisoridae diverged in the late Miocene about 12.2 Mya. The glyptosternoid clade was indicated to have diverged, also in the late Miocene, about 10.7 Mya, and the more specialized glyptosternoid genera, such as Pareuchiloglanis, originated in the Pleistocene (within 1.9 Mya). The speciation of glyptosternoid fishes is hypothesized to be closely related with the uplift of the Qinghai-Tibet Plateau.展开更多
Coryloideae consists of four genera: Corylus, Ostryopsis, Carpinus, and Ostrya. While both molecular and non-molecular data support the close relationship of Carpinus and Ostrya, the monophyly of the two genera has re...Coryloideae consists of four genera: Corylus, Ostryopsis, Carpinus, and Ostrya. While both molecular and non-molecular data support the close relationship of Carpinus and Ostrya, the monophyly of the two genera has remained controversial. In this study, sequences of the nuclear nitrate reductase (Nia) were used to test the naturalness of the two genera. Ostrya species form a robust clade, supporting the monophyly of the genus. The clade, however, is located between Carpinus cordata and the remaining species of Carpinus, indicating that Carpinus is paraphyletic, and Ostrya has evolved from within Carpinus. Within Carpinus, section Distegocarpus is polyphyletic, whereas section Carpinus is a clade where subsections Polyneurae and Carpinus are more closely related to each other than either is to subsection Monbeigianae.展开更多
Traditionally, Atraphaxis, Calligonum, Pteropyrum and Parapteropyrum are included in the tribe Atraphxideae. Recently, sequence data has revealed that this tribe is not monophyletic. The structure of the tribe was exa...Traditionally, Atraphaxis, Calligonum, Pteropyrum and Parapteropyrum are included in the tribe Atraphxideae. Recently, sequence data has revealed that this tribe is not monophyletic. The structure of the tribe was examined by adding more taxa and sequences to clarify the congruence between morphology and molecular phylogeny, the systematic placements of four genera in Polygonaceae, as well as the infra-generic relationships of Atraphaxis and Calligonum within Atraphaxideae. Five chloroplast genes, atpB-rbcL, psbA-trnH, trnL-tmF, psbK-psbl, and rbcL of Atraphaxis, Calligonum, Pteropyrum, and Parapteropyrum were sequenced. The non-monophyly of Atraphaxideae was confirmed. Atraphaxis and Calligonum, respectively, formed a monophyletic group that was well supported. Calligonum is closely related to Pteropyrum; Atraphaxis is sister to Polygonum s. str. and Parapteropyrum is allied with Fagopyrum. Although the morphology suggested the four genera should form a tribe, the molecular data indicated Atraphaxideae was not one monophyletic group. The clades identified within Atraphaxis corresponded well with the current sectional classification based on morphological features. As for Cal- ligonum, Medusa was identified as a non-monophyletic section.展开更多
Partial separation of a peripheral population may lead to its divergence and,potentially,speciation due to genetic drift followed by selection and geographic isolation.This process may cause taxonomic uncertainty beca...Partial separation of a peripheral population may lead to its divergence and,potentially,speciation due to genetic drift followed by selection and geographic isolation.This process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verifed directly.The two Nearctic allopatric species of magpies(Aves,Corvidae:Pica)serve as a good example of these problems.The Black-billed magpie Pica hudsonia is widely distributed in North America,whereas the Yellow-billed Magpie Pica nuttalli is endemic to a restricted range in California.Their relationships with Palearctic species have been little studied.We obtained complete mitochondrial genomes of both Nearctic magpie species,along with the Eurasian Magpie(Pica pica)and the Oriental Magpie(Pica serica),20 mitogenomes in total.Phylogenetic analysis reveals a basal position of P.serica,and P.pica as a sister clade to the two Nearctic species.P.hudsonia and P.nuttalli form reciprocal monophyletic subclades,showing recent divergence between and within them.Our data show that the Nearctic magpie lineage diverged from the common ancestor with P.pica,with a single migration wave via the Beringia.Within the Nearctic,we hypothesize a peripatric mode of speciation among Pica taxa due to the divergence and separation of the small marginal population in California below the Sierra-Nevada mountains.Diversifying amino acid substitutions in ND4-ND5-ND6 genes along the branch leading to the New World clade may indicate selection for heat-tolerance.Considering the clear phenotypic differences between P.hudsonia and P.nuttalli,our data,showing their reciprocal monophylies and genetic distinctness,is consistent with the two-species taxonomy.展开更多
Schistura heterognathos Chen,sp.nov.is described based on specimens from the Nanla River,a tri butary of the Lancangjiang River (upper Mekong River),in Yunnan Province of China.It is especially characterized by i...Schistura heterognathos Chen,sp.nov.is described based on specimens from the Nanla River,a tri butary of the Lancangjiang River (upper Mekong River),in Yunnan Province of China.It is especially characterized by its abnormal jaws.The jaws are broad,thick and strong.The upper jaw has no dentoid process and there is a very small or no notch in the lower jaw.The dissociative margins of jaws are straight.The mouth is broad and transversal,its width approximately equals to snout length and is greater than the interorbital width.展开更多
基金This work was supported by National Natural Sciences Foundation of China (No. 30160015).
文摘Sequences from the mitochondrial cytochrome b gene （Cyt b） were determined for 25 species from the superfamily Acridoidae and the homologous sequences of 19 species of grasshoppers were downloaded from the GenBank data library. The purpose was to develop a molecular phylogeny of the Acrypteridae, and to interpret the phylogenetic position of the family within the superfamily Acridoidea. Phylogeny was reconstructed by Maximum-parsimony （MP） and Bayesian criteria using Yunnanites coriacea and Tagasta marginella as outgroups. The alignment length of the fragments was 384 bp after excluding ambiguous sites, including 167 parsimony informative sites. In the fragments, the percentages of A ＋ T and G ＋ C were 70.7% and 29.3%, respectively. The monophyly of Arcypteridae is not supported by phylogenetic trees. Within the Arcypteridae, neither Arcypterinae nor Ceracrinae is supported as a monophyletic group. The current genus Chorthippus is not a monophyletic group, and should be a polyphyletic group. The present results are significantly different from the classification scheme of Arcypteridae, which is based on morphology.
基金supported by the National Basic Research Program of China(973 ProgramGrant No.2013CB834100)
文摘We describe an interactive viewer for the All-Species Living Tree（LVTree）. The viewer incorporates treeing and lineage information from the ARB-SILVA website. It allows collapsing the tree branches at different taxonomic ranks and expanding the collapsed branches as well, keeping the overall topology of the tree unchanged. It also enables the user to observe the consequence of trial lineage modifications by re-collapsing the tree. The system reports taxon statistics at all ranks automatically after each collapsing and re-collapsing. These features greatly facilitate the comparison of the 16 S rRNA sequence phylogeny with prokaryotic taxonomy in a taxon by taxon manner.In view of the fact that the present prokaryotic systematics is largely based on 16 S rRNA sequence analysis, the current viewer may help reveal discrepancies between phylogeny and taxonomy. As an application, we show that in the latest release of LVTree, based on 11,939 rRNA sequences, as few as 24 lineage modifications are enough to bring all but two phyla（Proteobacteria and Firmicutes） to monophyletic clusters.
基金supported by the National Natural Science Foundation of China (Grant No. 31090254)
文摘Nineteen taxa representing 10 genera of Sisoridae were subjected to phylogenetic analyses of sequence data for the nuclear genes Plagl2 and ADNP and the mitochondrial gene cytochrome b. The three data sets were analyzed separately and combined into a single data set to reconstruct phylogenetic relationships among Chinese sisorids. Both Chinese Sisoridae as a whole and the glyptosternoid taxa formed monophyletic groups. The genus Pseudecheneis is likely to be the earliest diverging extant genus among the Chinese Sisoridae. The four Pareuchiloglanis species included in the study formed a monophyletic group. Glaridoglanis was indicated to be earliest diverging glyptosternoid, followed by Glyptosternon maculatum and Exostoma labiatum. Our data supported the conclusion that Oreoglanis and Pseudexostoma both formed a monophyletic group. On the basis of the fossil record and the results of a molecular dating analysis, we estimated that the Sisoridae diverged in the late Miocene about 12.2 Mya. The glyptosternoid clade was indicated to have diverged, also in the late Miocene, about 10.7 Mya, and the more specialized glyptosternoid genera, such as Pareuchiloglanis, originated in the Pleistocene (within 1.9 Mya). The speciation of glyptosternoid fishes is hypothesized to be closely related with the uplift of the Qinghai-Tibet Plateau.
基金The Third Phase of the Innovation Program in the Chinese Academy of SciencesGrants from the National Natural Science Foundation of China (Grant Nos.30670242 and 30500056)the Major Program from the Natural Science Foundation,Beijing(6081002)
文摘Coryloideae consists of four genera: Corylus, Ostryopsis, Carpinus, and Ostrya. While both molecular and non-molecular data support the close relationship of Carpinus and Ostrya, the monophyly of the two genera has remained controversial. In this study, sequences of the nuclear nitrate reductase (Nia) were used to test the naturalness of the two genera. Ostrya species form a robust clade, supporting the monophyly of the genus. The clade, however, is located between Carpinus cordata and the remaining species of Carpinus, indicating that Carpinus is paraphyletic, and Ostrya has evolved from within Carpinus. Within Carpinus, section Distegocarpus is polyphyletic, whereas section Carpinus is a clade where subsections Polyneurae and Carpinus are more closely related to each other than either is to subsection Monbeigianae.
基金supported by Chinese Academy of Sciences Important Direction for Knowledge Innovation Project (KZCX2-EW-305),Xinjiang Institute of Ecology and Geography,Chinese Academy of Sciences
文摘Traditionally, Atraphaxis, Calligonum, Pteropyrum and Parapteropyrum are included in the tribe Atraphxideae. Recently, sequence data has revealed that this tribe is not monophyletic. The structure of the tribe was examined by adding more taxa and sequences to clarify the congruence between morphology and molecular phylogeny, the systematic placements of four genera in Polygonaceae, as well as the infra-generic relationships of Atraphaxis and Calligonum within Atraphaxideae. Five chloroplast genes, atpB-rbcL, psbA-trnH, trnL-tmF, psbK-psbl, and rbcL of Atraphaxis, Calligonum, Pteropyrum, and Parapteropyrum were sequenced. The non-monophyly of Atraphaxideae was confirmed. Atraphaxis and Calligonum, respectively, formed a monophyletic group that was well supported. Calligonum is closely related to Pteropyrum; Atraphaxis is sister to Polygonum s. str. and Parapteropyrum is allied with Fagopyrum. Although the morphology suggested the four genera should form a tribe, the molecular data indicated Atraphaxideae was not one monophyletic group. The clades identified within Atraphaxis corresponded well with the current sectional classification based on morphological features. As for Cal- ligonum, Medusa was identified as a non-monophyletic section.
基金supported by a grant from the Harvard Global Institute for research on biodiversity of ChinaThe research was carried out within the state assignment of Ministry of Science and Higher Education of the Russian Federation(theme No.121031500274-4)。
文摘Partial separation of a peripheral population may lead to its divergence and,potentially,speciation due to genetic drift followed by selection and geographic isolation.This process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verifed directly.The two Nearctic allopatric species of magpies(Aves,Corvidae:Pica)serve as a good example of these problems.The Black-billed magpie Pica hudsonia is widely distributed in North America,whereas the Yellow-billed Magpie Pica nuttalli is endemic to a restricted range in California.Their relationships with Palearctic species have been little studied.We obtained complete mitochondrial genomes of both Nearctic magpie species,along with the Eurasian Magpie(Pica pica)and the Oriental Magpie(Pica serica),20 mitogenomes in total.Phylogenetic analysis reveals a basal position of P.serica,and P.pica as a sister clade to the two Nearctic species.P.hudsonia and P.nuttalli form reciprocal monophyletic subclades,showing recent divergence between and within them.Our data show that the Nearctic magpie lineage diverged from the common ancestor with P.pica,with a single migration wave via the Beringia.Within the Nearctic,we hypothesize a peripatric mode of speciation among Pica taxa due to the divergence and separation of the small marginal population in California below the Sierra-Nevada mountains.Diversifying amino acid substitutions in ND4-ND5-ND6 genes along the branch leading to the New World clade may indicate selection for heat-tolerance.Considering the clear phenotypic differences between P.hudsonia and P.nuttalli,our data,showing their reciprocal monophylies and genetic distinctness,is consistent with the two-species taxonomy.
文摘Schistura heterognathos Chen,sp.nov.is described based on specimens from the Nanla River,a tri butary of the Lancangjiang River (upper Mekong River),in Yunnan Province of China.It is especially characterized by its abnormal jaws.The jaws are broad,thick and strong.The upper jaw has no dentoid process and there is a very small or no notch in the lower jaw.The dissociative margins of jaws are straight.The mouth is broad and transversal,its width approximately equals to snout length and is greater than the interorbital width.
